
Part A: Network Analysis with Cytoscape
Goals and Motivations
By the end of these sessions you should be able to:
- Understand the major applications of network biology
- Find relevant networks and pathways
- Import your data into Cytoscape
- Perform basic topological and other network analyses
- Master network layouts and data visualization
- Know where to find relevant Cytoscape apps and tutorials
- Be able to analyze scRNA-seq data using Cytoscape - Only resource
provided.
Introduction to Network Biology
Why Networks?
Networks are everywhere… especially in biology!
- Molecular networks
- Understand the major applications of network biology
- Find relevant networks and pathways
- Cell-cell communication
- Nervous systems
- Social networks
Single Cell Transcriptomics

Proteomics

Biological Network Taxonomy
Pathways
- Metabolic
- Signaling
- Regulatory
- Disease

Interactions

Similarity

We will now go to the next session (1 B) to understand terms about
public repositories.
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